SQANTI3 Analysis: complete transcriptome

Reference: Shared reference drawing used for all categories.

FSM (Full Splice Match): The reference and query isoform have the same number of exons and each internal junction agree. The exact 5' start and 3' end can differ by any amount.

ISM (Incomplete Splice Match): The query isoform has fewer 5' exons than the reference, but each internal junction agree. The exact 5' start and 3' end can differ by any amount.

NIC (Novel In Catalog): The query isoform does not have a FSM or ISM match, but is using a combination of known donor/acceptor sites.

NNC (Novel Not in Catalog): The query isoform does not have a FSM or ISM match, and has at least one donor or acceptor site that is not annotated.

Genic Genomic: The query isoform overlaps with introns and exons.

Antisense: The query isoform does not overlap a same-strand reference gene but is anti-sense to an annotated gene.

Fusion: The query isoform spans two or more annotated genes.

Intergenic: The query isoform is in the intergenic region.

Genic Intron: The query isoform is completely contained within an annotated intron.

Structural Categories: All structural categories and definitions are shown below.

For more details on categories, visit here: SQANTI3 Wiki: Categories.
For a detailed explanation of each column of the table (SQANTI3 classification), see here: Column Glossary.

How to Filter:

Numeric Columns (e.g., length, exons): Use ranges like 100:1000 (values between 100 and 1000), 100: (>100), or :1000 (<1000). Single numbers perform an exact match.
Dropdowns: Select a value to filter for an exact match.
Text Columns: Type to search for substrings (case-insensitive).

Generate Trix String (for UCSC Genome Browser search):

Use dropdown filters and click "Generate Trix String" to get a search based on your filter criteria.
Note: Range filters (e.g., 100:1000) are not supported by Trix and will be ignored, only exact numeric matches are supported.
Search terms automatically use underscores (e.g., structural_category_full_splice_match, strand_plus, coding_coding).
Click rows to select (click again to deselect). Multiple rows can be selected. Then click "Generate Trix String" to get search terms.

Generate Filter String (for Table Browser):

Select one or more rows (or apply filters to narrow the table), then click "Generate Filter String" to get a newline-separated list of isoform IDs.
Copy the list and paste (one ID per line) into UCSC Table Browser when filtering the track by the name field to create a custom track with only those isoforms.